I attempted to do a cash out refi into my LLC, and was told all i needed was to add my mother as a minority member to my LLC to properly transfer the deed.   

Get a builder quote from at least 3 LOCAL builders or Renovation Contractors first, then weight your available options. 

Now we’re buying a second property to use as an STR, and I’m afraid we’re going to have a huge mess at tax time if we don’t get proper guidance.

Short Term Rentals are great but it takes a significant amount of upfront work and cost to execute them properly. 

Take ownership of your mistake and learn to do the proper due diligence recommended above😊

Make sure the “guts” of the toilets are working properly.

The one set of tenants did not even bat an eye (had not had a rent increase in 7+ years prior), and the other set appreciated it and moved out about 2 months after the rent increase (with proper notice). 

HOWEVER, if you already knew about a pre-existing roach issue and maybe failed to disclose it to them properly/didn't set correct expectations when they moved in, then it's on you. 

Do you have a weight limit on dogs to keep the potential "dangerous" breeds away, or do you find that most folks don't travel with their 100 lb Rotty?

Proper transparent accounting is essential to any partnership, including when partnership is family.